Gene-disabling techniques simplified by Stanford team

STANFORD, Calif. - Sometimes the first step to learning a gene's role is to disable it and see what happens. Now researchers at the Stanford University School of Medicine have devised a new way of halting gene expression that is both fast and cheap enough to make the technique practical for widespread use. This work will accelerate efforts to find genes that are involved in cancer and the fate of stem cells, or to find genes that make good targets for therapeutic drugs.

The technique, published in the February issue of Nature Genetics and now available online, takes advantage of small molecules called short interfering RNA, or siRNA, which derail the process of translating genes into proteins. Until now, these molecular newcomers in genetics research have been difficult and expensive to produce. Additionally, they could impede the activity of known genes only, leaving a swath of genes in the genetic hinterlands unavailable for study.

"siRNA technology is incredibly useful but it has been limited by expense and labor. A better method for generating siRNA has been needed for the whole field to move forward," said study leader Helen Blau, PhD, the Donald E. and Delia B. Baxter Professor of Pharmacology. She said some companies are in the process of creating pools, or libraries, of siRNA molecules for all known genes in specific organisms but these libraries aren't yet available.

Pathology graduate students George Sen, Tom Wehrman and Jason Myers became interested in creating siRNA molecules as a way of screening for genes that alter the fate of stem cells - cells that are capable of self-renewal and the primary interest of Blau's lab. The students hoped to block protein production for each gene to find out which ones play a critical role in normal stem cell function.

"I told them that creating individual siRNAs to each gene was too expensive," said Blau. Undaunted, the students came up with a protocol for making an siRNA library to obstruct expression of all genes in a given cell - including genes that were previously uncharacterized. They could then pull individual molecules like books from a shelf to test each one for a biological effect.

The team had several hurdles to overcome in developing their protocol. The first was a size limit - an siRNA molecule longer than 29 subunits causes wide-ranging problems in the cell. The key to overcoming this barrier was a newly available enzyme that snips potential siRNA molecules into 21-subunit lengths. A further step copied these short snippets into a form that could be inserted into a DNA circle called a plasmid. When the researchers put a single plasmid into a cell, it began churning out the gene-blocking siRNA molecule.

The group tested their approach by creating a handful of siRNA molecules to genetically disable three known genes. In each case, their technique generated siRNA that effectively blocked the gene in question.
Wehrman said this technique of creating siRNA molecule libraries could be widely used to find genes that, when disabled, cause cells to become cancerous or alter how the cells respond to different drugs. These genes could then become potential targets for drugs to treat disease.

A paper in the same issue of Nature Genetics described a similar way of creating siRNA libraries. "Having two unrelated groups working on the same problem shows there has been a real need for the technology," Blau said. The Stanford group has filed a patent for its technique.

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Stanford University Medical Center integrates research, medical education and patient care at its three institutions - Stanford University School of Medicine, Stanford Hospital & Clinics and Lucile Packard Children's Hospital at Stanford. For more information, please visit the Web site of the medical center's Office of Communication & Public Affairs at http://mednews.stanford.edu.

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